Depends on what output aspect ratio and which video arrangd method you pick. If the source is NTSC, and if the output is 16:9, then you can select either one (16:9 Display or 16:9 NTSC), and the result should be exactly the same.

If you are converting from 16:9 to 4:3, or resizing the image in some other way, TMPGEnc needs to know the pixel aspect ratio, and it determines this based on the option you choose. Although the image in 16:9 PAL has the same aspect ratio as in 16:9 NTSC, the pixel aspect ratio isn't the same.